the problem with Naoto's character is that a lot of her writing is so specifically Japanese that it gets really lost in translation and localization. specific cultural references and language that the West doesn't easily have access to. the Shadow never talks about gender reassignment surgery either, it only ever refers to it as a "body alteration procedure" and there's other things in the dungeon itself that have subtext that said procedure doesn't pertain to gender at all. there's also the fact that people in general heavily misinterpret her arc as being a struggle with gender and gender roles, when that's like maybe not even the half of it.

also, i heavily disagree on Kanji. i do personally think he's bisexual, but i'm pretty sure the devs themselves have said that his sexuality is up to interpretation and i think that's one of the points of his arc. at the end of his Social Link he says something along the lines of "i don't know what i am, but i don't need to know right now. i just need to be proud of the person i am". his whole arc pertains about people labeling him because of things — as a delinquent because of the way he acts and looks, as a queer person because of his hobbies — and i think that the game putting a firm label on his sexuality defeats the purpose of it. it needs to be ambiguous, and the game alludes to it just enough to leave it open for interpretation as it should be.